- BioRxiv Biochemistry
- BioRxiv Bioinformatics
- BioRxiv Biophysics
- BioRxiv Cancer Biology
- BioRxiv Pharmacology and Toxicology
- BioRxiv Systems Biology
- BioRxiv Zoology
- by Aazmi, O., Aswale, A. R., Chugh, J.Proteins exist as dynamic ensembles, with their native states comprising interconverting conformational substates critical to their physiological functions and participation in disease states. Fused in Sarcoma (FUS), an RNA-binding protein implicated in neurodegenerative diseases such as Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD), contains an RNA recognition motif (RRM) known to form fibrillar aggregates. Here, we investigate the conformational plasticity of FUS-RRM in its native state using advanced NMR techniques, particularly 15N chemical exchange saturation transfer and heteronuclear adiabatic […]
- by Roques, M., Niu, C., Brochet, M., Brusini, L. A.Faithful chromosome segregation relies on precise kinetochore-microtubule interactions and checkpoint surveillance, yet the molecular basis of these processes varies widely across eukaryotes and is only beginning to be defined in apicomplexan parasites. In the malaria parasite Plasmodium berghei, chromosome segregation is especially critical during transmission from host to mosquito: rapid mitoses generate male gametes, and subsequent meiosis in the zygote seeds the next generation of infection. Here, we identify Aurora-related kinase 1 (ARK1) as a central regulator of chromosome segregation […]
- by Wilbanks, L. E., Roberts, C. B., Frias-Gomez, M., Hennigan, H. E., Castator, K. G., Budimir, Z. L., Zu, C., Parkinson, E. I.The soil dwelling bacteria Streptomyces is an abundant producer of numerous anticancer, antifungal, and antibiotic compounds (i.e. Natural Products, NPs). The sophisticated cellular machinery required to produce NPs is frequently regulated by quorum-sensing systems, consisting of cluster situated regulators (CSRs), such as TetR-like repressors, and small-molecule autoregulator (AR) ligands. Only a small fraction of bioinformatically predicted quorum-sensing AR circuits have been experimentally determined, and fewer still have been engineered as inducible expression systems for synthetic biology. This research details the […]
- by Mehlan, H., Hirschmann, S., Busch, L. M., Hennig, A., Nieselt, K., Völker, U., Hammerschmidt, S., Mäder, U.The Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen that exhibits more than 100 different capsular serotypes and considerable genomic variation. S. pneumoniae is also an important model organism for basic and biomedical research, with a number of strains with different characteristics being used. To address this, we have created the manually curated pan-genome database PneumoWiki (https://pneumowiki.med.uni-greifswald.de) that integrates genomic data from 43 S. pneumoniae strains with various aspects of functional annotation. All data relating to a specific gene […]
- by Fernandes Hartzig, L. M., Peringathara, S., Darisipudi, M. N., Seegert, S. L. L., Bludau, E., Weiss, S., Vogelgesang, A., Schoon, J., Corleis, B., Dorhoi, A., Broker, B. M., Holtfreter, S.Individuals colonized with the pathobiont Staphylococcus aureus can develop endogenous S. aureus infections if the delicate balance between host and microbe is disturbed. We have recently developed a model of persistent S. aureus colonization using the mouse-adapted S. aureus strain JSNZ. This strain is efficiently transferred from the parents to the offspring, leading to lifelong and usually asymptomatic colonization. Here we report that adult male mice frequently develop spontaneous infections of their preputial glands (preputial gland adenitis, PGA), which are […]
- by Dai, D., Zhang, S., Hu, B., Zhou, Y., Cui, S., Sun, J., Zhang, Y., Wang, X., Siddique, S., Bo, D., Zhang, M., Williamson, V. M., Yao, H., Duan, X., Wu, W., Peng, D., Zheng, J., Sun, M.The study of the global regulatory mechanisms controlling pathogen virulence gene expression is key to understanding the underlying mechanisms of pathogenicity. 6mA plays a critical role in regulating gene expression in response to various environmental stresses, but its biological functions related to pathogen virulence remain largely unexplored. We report the widespread presence of 6mA across 17 isolates of nematodes, along with an exploration of the 6mA landscape in the genomes of six notorious agricultural pathogen root-knot nematodes (RKNs). Our results […]
- by DATT, T., Datt, S., Singh, S., Singh, N.Background: Third generation Cephalosporins resistances among Escherichia coli due to production of ESBL, mainly the bla-CTX-M, bla-TEM and bla-SHV genes, poses serious challenges in the clinical utility of these drugs in healthcare settings. This study was undertaken to detect prevalence of ESBL producing MDR E. coli isolates by various phenotypic and molecular method from in or out patients with urinary tract infection (UTI). Methods: A total of 56 non-repetitive isolates of E. coli from in or out patients of UTI […]
- by Virdee, S., Fletcher, A. J., Squair, D. R., Rivers, E., Sowar, H., Balci, A., Harmo, R., Wright, D. J., Beniwal, G., Soetens, M., Mathur, S., Tollervey, A., Stanton, C.The detection of viral RNA inside cells triggers a diverse range of antiviral responses, including global translation inhibition, interferon secretion and RNA sequestration. Mutations in the gene ZNFX1 cause severe paediatric immunodeficiencies, including chronic viral infection and autoinflammation. Here, we show that ZNFX1 is an RNA helicase with cryptic and unusual bifurcating E3 ubiquitin ligase activity. Nucleotide-dependent RNA binding stimulates ZNFX1 to generate complex ubiquitin chains via a two-component ubiquitin circuit wired in parallel, with ubiquitin flux occurring via either […]
- by Agrawal, N., Parisini, E.Semen-derived enhancer of viral infection (SEVI) fibrils, assembled from the peptide fragment PAP248-286, enhance HIV transmission by promoting viral attachment to host cells. However, the molecular basis of SEVI nucleation and early aggregation remains unclear. Here, we conducted 80 independent all-atom molecular dynamics (MD) simulations spanning a total of 40 s, together with 100 independent steered MD and umbrella sampling runs, to explore the dimerization and dissociation of PAP248-286 Our results show that hydrogen bonding is the dominant stabilizing force […]
- by Laurans, S., Huerre, S., Dellis, O., Ferard, C., Jalaber, H., Vanbergue, C., Brun, E., Jelin, R., Nüsse, O., Benihoud, K., Dupre-Crochet, S.Adenoviruses are common pathogens that have been engineered and used for medical purposes. Their recognition by innate immune cells such as macrophages and dendritic cells has been widely studied, but very little information is available on adenovirus interaction with neutrophils. Using cytometry and confocal and electron microscopy, we showed that neutrophils bind to antibody-coated adenoviruses and engulf them in a phagosome. Using a single-cell transcriptomic approach, we found that adenovirus phagocytosis activates a specific transcriptional program in neutrophils. It also […]
- by Uchida, S., Hagihara, M., Inoue, K., Abe, T., Sakurai, T., Miyamichi, K.Thermogenesis is critical for survival and health in mammals. Although the thermoregulatory systems in the preoptic area are well documented, the downstream processing of these central signals–particularly by medullary neurons involved in the control of shivering and sympathetic activation of brown adipose tissue (BAT)–remains incompletely understood. Here we show that vesicular glutamate transporter type 3 (vGluT3)-expressing neurons in the medullary raphe pallidus (RPa) become active immediately before a spontaneous increase in body temperature. These neurons remain inactive under experimentally induced […]
- by Baguette, M., Le Floch, G., Bels, V., Schtickzelle, N., Hernandez–Posseme, L.Modification of phenotypic traits induced by character displacements allow species to coexist by reducing interspecific competition. This study explores if and how shorebirds partition feeding resources by foraging at different water depths outside the breeding season. During this period, communities of up to dozen shorebird species coexist on suitable habitats at land-water interfaces. By video recording 22 species of migrating and wintering shorebirds in different sites, we show that their distribution according to the water height at which they forage […]
- by Dicksion, C. A., Chao, D. N., Rickmeyer, J. D., Bess, E. N.The human gut microbiome is home to numerous small molecules that impact health. Three prominent classes of molecules in this environment include phenolic acids, lignans, and enterolignans, which have been linked to anti-inflammatory and anti-oxidant effects as well as protection from cancer, cardiovascular disease, and neurodegeneration. The abundance of these molecules in the gut microbiome as well as their biological significance motivated the development of the LC-MS/MS method reported herein, which provides a simple, robust, and high-throughput approach to simultaneously […]
- Mitochondria Clearance Enables Macrophage-Driven Maturation of iPSC-Derived Cardiomyocyte Metabolismby Ketchum, F., Celebi, L. E., Hawthorne, L., Zorlutuna, P.Generation of functional engineered myocardial tissue remains a challenge, owing in part to lacking maturity of stem cell-derived cardiomyocytes. Current strategies to mature these cells fall short of achieving in vivo-like physiology. Macrophages, members of the innate immune system, reside in the heart and exert positive effects on cardiomyocyte function. We hypothesized that developmentally informed addition of macrophages to cardiomyocytes would improve their maturity. While some recent studies have added macrophages to stem cell-derived models of the human myocardium, these […]
- by Kindree, K., Chochinov, C. A., Bhachu, K., Cheng, Y., Caron, A., McDonald, M., Mamai, Z., Nguyen Ba, A. N.The analysis of gene function frequently requires the generation of mutants. Deep-mutational scanning (DMS) has emerged as a powerful tool to decipher important functional residues within genes and proteins. However, methods for performing DMS tend to be complex or laborious. Here, we introduce Tiled-Region Exchange (T-REx) Mutagenesis, which is a multiplexed modification of the EMPIRIC mutagenesis approach. Self-encoded removal fragments are cloned in parallel in non-overlapping gene locations and pooled. In a one-pot reaction, oligonucleotides are then swapped with their […]
- by Gorssen, W., Kadri, N. K., Khayatzadeh, N., Leonard, A. S., He, Q., Mehrotra, A., Neuenschwander, S., Pausch, H.Iris pigmentation is a heritable trait with a complex genetic architecture. While the genetic basis of iris pigmentation has been extensively studied in humans, little is known about iris pigmentation in pigs. Iris pigmentation in pigs varies from different shades of brown or pale irises to heterochromia manifesting either as different colors between both irises (heterochromia iridum) or multiple colors within a single iris (heterochromia iridis). This study investigates the genetics of iris pigmentation variability in the Swiss Landrace and […]
- by Carlier, A., Barthelemy, I., Blanchard-Gutton, N., Chateau-Joubert, S., aurade, F., Ozturk, T., Didier, N., Relaix, F., Tiret, L., Blot, S., Punzon, I.We determined the potential of CRISPR/Cas13 technology as a therapeutic approach for centronuclear myopathies (CNMs) by reducing the expression of a single protein, DNM2. CNMs are severe congenital rare muscle disorders that result in muscle hypotrophy and weakness, with no cure. CNMs frequently result from mutations in either BIN1, MTM1, or DNM2 genes, with DNM2 being a key GTPase that plays a pivotal role in muscle membrane interactions with MTM1 and BIN1. Previous studies indicate that reducing DNM2 transcript expression […]
- by Mikkola, L., Boluk, A., Piipponen, M., Mikocziova, I., Valkonen, M., Fagersund, J., Hakovirta, H., Saraste, A., Hernandez de Sande, A., Palani, S., Ord, T., Roivainen, A., Ruusuvuori, P., Heinaniemi, M., Kaikkonen, M. U., Lonnberg, T.Background Atherosclerosis is a common disorder where changes in vascular wall and in the surrounding perivascular adipose tissue are evident. However, how multiple cell types contribute to the disease at the cellular level remains poorly understood. Moreover, obesity can exacerbate atherogenesis, but it remains to be revealed which cell types drive the aggravation. Our objectives were to define the key cell populations across tissues in a highly atherogenic mouse model of atherosclerosis under obese and normal-weight conditions, and to explore […]
- by Selvan, N. P., Mukherjee, A., Erben, E., Kim, H.-S.Trypanosoma brucei is a protozoan parasite that causes African trypanosomiasis. We performed an overexpression library screen to gain insights into essential cellular processes in T. brucei and identified genes whose overexpression impaired parasite growth. One of the three top-ranking candidates we validated exhibited a notable phenotype. TbFOP, an uncharacterized protein, has an N-terminal arginine-rich domain and a C-terminal FOP (Friend Of PRMT1) domain. TbFOP overexpression substantially increases antisense transcription across the genome, particularly at Transcription Termination Sites (TTSs). This phenotype […]
- by Martino, F., Cooper, C., Newton, J., Bateman, P., Kestel, J., van der Heyde, M., Allentoft, M., Mousavi-Derazmahalleh, M., Lawrie, A., Guthrie, A., Nevill, P.Air is receiving increasing recognition as a biologically rich source of taxonomically diverse environmental DNA (eDNA). Multiple proof-of-concept studies have explored air as a medium for the detection of single terrestrial species, and even entire terrestrial communities, including mammals, non-anemophilous plants and insects. Airborne eDNA has been sampled using various stationary devices but if we can access it using mobile collection methods, we can rapidly assess biodiversity at large spatial scales. We therefore compared passive eDNA filters deployed for short […]